Grant‐in‐Aid for Scientific Research on Innovative Areas
(Research in a proposed research area)

Novel measurement techniques forvisualizing 'live' protein molecules at work

Achivements

The number of research papers published every year
5 in 2014 / 56 in 2015 / 82 in 2016 / 63 in 2017 / 84 in 2018 / 45 in 2019
335 in Total

2015

Papers in 2015

1.
Structural elucidation of an asparagine-linked oligosaccharide from the hyperthermophilic archaeon, Archaeoglobus fulgidus.
Fujinami D, Nyirenda J, Matsumoto S, *Kohda D.
Carbohydr Res 413, 55-62 (2015).
2.
N-Glycosylation with synthetic undecaprenyl pyrophosphate-Linked oligosaccharide to oligopeptides by PglB oligosaccharyltransferase from Campylobacter jejuni
Ishiwata A, Taguchi Y, Lee YJ, Watanabe T, Kohda D, *Ito Y
Chembiochem 16 , 731-737 (2015).
3.
Structural analysis of the mechanism of phosphorylation of a critical autoregulatory tyrosine residue in FGFR1 kinase domain
Kobashigawa Y, Amano S, Yokogawa M, Kumeta H, Morioka H, Inouye M, Schlessinger J, *Inagaki F
Genes Cells 20 , 860-870 (2015).
4.
Ligand-driven conformational changes of MurD visualized by paramagnetic NMR
Saio T, Ogura K, Kumeta H, Kobashigawa Y, Shimizu K, Yokochi M, Kodama K, Yamaguchi H, Tsujishita H, *Inagaki F
Sci Rep 5 , 16685 (2015).
5.
Method of mechanical holding of cantilever chip for tip-scan high-speed atomic force microscopy
Fukuda S, Uchihashi T, *Ando T
Rev Sci Instrum 86 , 063703 (2015).
6.
Investigation of the redox-dependent modulation of structure and dynamics in human cytochrome c
Imai M, Saio T, Kumeta H, Uchida T, Inagaki F, *Ishimori K
Biochem Biophys Res Commun 469 , 978-984 (2015).
7.
Ligand-driven conformational changes of MurD visualized by paramagnetic NMR
Saio T, Ogura K, Kumeta H, Kobashigawa Y, Shimizu K, Yokochi M, Kodama K, Yamaguchi H, Tsujishita H, *Inagaki F
Sci Rep 5 , 16685 (2015).
8.
One-dimensional sliding of p53 along DNA is accelerated in the presence of Ca2+ or Mg2+ at millimolar concentrations
Murata A, Ito Y, Kashima R, Kanbayashi S, Nanatani K, Igarashi C, Okumura M, Inaba K, Tokino T, *Takahashi S, *Kamagata K
J Mol Biol 427 , 2663-2678 (2015).
9.
Complexity of the folding transition of the B domain of protein A revealed by the high-speed tracking of single-molecule fluorescence time series
Oikawa H, Kamagata K, Arai M, *Takahashi S
J Phys Chem B 119 , 6081-6091 (2015).
10.
Structural Stability of Amyloid Fibrils Depends on the Existence of the Peripheral Sequence near the Core Cross-03B2 Region
*Saiki M, Shiba K, Okumura M
FEBS Lett. 589 , 3541-3547 (2015).
11.
A PDI-catalyzed thiol/disulfide switch regulates the production of hydrogen peroxide by human Ero1
Ramming T, Okumura M, Kanemura S, Baday S, Birk J, Moes S, Jenö P, Bernèche S, Inaba K, *Appenzeller-Herzog C
Free Radic Biol Med. 83 , 361-372 (2015).
12.
One-dimensional sliding of p53 along DNA is accelerated in the presence of Ca2+ or Mg2+ at millimolar concentrations
Murata A, Ito Y, Kashima R, Kanbayashi S, Nanatani K, Igarashi C, Okumura M, Inaba K, Tokino T, *Takahashi S, *Kamagata K
J. Mol Biol. 427 , 2663-2678 (2015).
13.
Structural and mechanistic basis of the PDI family members producing disulfides within the ER
Okumura M, Kadokura H, *Inaba K
Free Radic Biol Med. 83 , 314-322 (2015).
14.
Axonemal dynein light chain-1 locates at the microtubule-binding domain of the γ heavy chain
Ichikawa M, Saito K, Yanagisawa H, Yagi T, Kamiya R, Yamaguchi S, Yajima J, Kushida Y, Nakano K, Numata O and *Toyoshima YY
Molecular Biology of the Cell 26 , 4236-4247 (2015).  
15.
K+-responsive off-to-on switching of hammerhead ribozyme through dual G-quadruplex formation requiring no heating and cooling treatment
Yamaoki Y, Nagata T, Mashima T, *Katahira M
Biochem Biophys Res Commun 468 , 27-31 (2015).
16.
The binding specificity of translocated in liposarcoma/fused in sarcoma with lncRNA transcribed from the promoter region of cyclin D1
Yoneda R, Suzuki S, Mashima T, Kondo K, Nagata T, Katahira M, *Kurokawa R
Cell Biosci 6 , DOI: 10.1186/s13578-016-0068-8 (2015). 
17.
Protein response to chromophore isomerization in microbial rhodopsins revealed by picosecond time-resolved ultraviolet resonance Raman spectroscopy: a review
Mizuno M, *Mizutani Y
In Recent Progress in Surface and Colloids Chemistry with Biological Applications (ACS Symposium Series) 1215 , 329-353 (2015).
18.
Structural basis for energy transfer pathways in the plant PSI-LHCI super-complex
Qin X, Suga M, *Kuang T, *Shen JR
Science 348 , 989-995 (2015).
19.
Lis1 restricts the conformational changes in cytoplasmic dynein on microtubules
Toba S, Koyasako K, Yasunaga T, Hirotsune S. Toba S, Koyasako K, Yasunaga T, Hirotsune S
Microscopy 64 , 419-427 (2015).
20.
Synergistic effect of ATP for RuvA-RuvB-Holliday junction DNA complex formation
Iwasa, T., Han, Y. W., Hiramatsu, R., Yokota, H., Nakao, K., Yokokawa, R., Ono, T., *Harada, Y.
Sci. Rep. 5 , 18177 (2015).
21.
Structural Basis of the Differential Function of the Two C. elegans Atg8 Homologs, LGG-1 and LGG-2, in Autophagy
Wu F, Watanabe Y, Guo XY, Qi X, Wang P, Zhao HY, Wang Z, Fujioka Y, Zhang H, Ren JQ, Fang TC, Shen YX, Feng W, Hu JJ, *Noda NN, *Zhang H
Mol. Cell 60 , 914-929 (2015).
22.
Atg1 family kinases in autophagy initiation
*Noda NN, Fujioka Y
Cell. Mol. Life Sci. 72 , 3083-3096 (2015).
23.
Nucleosome compaction facilitates HP1γ binding to methylated H3K9
Mishima Y, Jayasinghe CD, Lu K, Otani J, Shirakawa M, Kawakami T, Kimura H, Hojo H, Carlton P, Tajima S, *Suetake I
Nucleic Acids Res 43 , 10200-10212 (2015).
24.
Suppression of nonspecific protein-nanodiamond adsorption enabling specific targeting of nanodiamonds to biomolecules of interest
Sotoma S, Igarashi R , Iimura J, Kumiya Y , Tochio H, Harada Y, *Shirakawa, M
Chem Lett 44 , 354-356 (2015).
25.
Optically detected nagnetic resonance of nanodiamonds in vivo; implementation of selective imaging and fast sampling
*Yoshinari Y, Mori S, Igarashi R, Sugi T, Yokota H, Ikeda K, Sumiya H, Mori I, Tochio H, *Harada Y, Shirakawa M
J Nanosci Nanotechnol 15 , 1014-1021 (2015).
26.
Comprehensive and quantitative analysis for controlling the physical/chemical states and particle properties of nanodiamonds for biological applications
Sotoma S, Akagi K, Hosokawa S, Igarashi R, Tochio H, Harada Y, *Shirakawa, M
RSC ADVANCES 5 , 13818-13(2015).
27.
The unexpected role of polyubiquitin chains in the formation of fibrillar aggregates
Morimoto D, Walinda E, Fukada H, Sou YS, Kageyama S, Hoshino M, Fujii T, Tsuchiya H, Saeki Y, Arita K, Ariyoshi M, Tochio H, Iwai K, Namba K, Komatsu M, Tanaka K, *Shirakawa M
Nat Commun 6 , 6116 (2015).
28.
Magnetic resonance imaging of tumor with a self-traceable phosphorylcholine polymer
Yamada H, Hasegawa Y, Imai H, Takayama Y, Sugihara F, Matsuda T, Tochio H, Shirakawa M, Sando S, Kimura Y, Toshimitsu A, *Aoyama Y, *Kondo T
J Am Chem Soc. 137 , 799-806 (2015).
29.
Mechanical force effect on the two-state equilibrium of the hyaluronan-binding domain of CD44 in cell rolling
Suzuki T, Suzuki S, Umemoto R, Ogino S, Nishida N, *Shimada I
Proc Natl Acad Sci U S A 112 , 6991-6996 (2015).
30.
Differential Large-Amplitude Breathing Motions in the Interface of FKBP12-Drug Complexes
Yang CJ, Takeda M, Terauchi T, Jee J, *Kainosho M
Biochemistry 54 , 6983-95 (2015).
31.
Nano-mole scale sequential signal assignment by 1H-detected protein solid-state NMR
Wang S, Parthasarathy S, Xiao Y, Nishiyama Y, Long F, Matsuda I, Endo Y, Nemoto T, Yamauchi K, Asakura T, Takeda M, Terauchi T, Kainosho M, *Ishii Y
Chem Commun (Camb) 51 , 15055-15058 (2015).
32.
Nano-mole scale side-chain signal assignment by 1H-detected protein solid-state NMR by ultra-fast magic-angle spinning and stereo-array isotope labeling
Wang S, Parthasarathy S, Nishiyama Y, Endo Y, Nemoto T, Yamauchi K, Asakura T, Takeda M, Terauchi T, Kainosho M, *Ishii Y
PLoS One 10 , e0122714 (2015).
33.
Reconstitution of the targeting of Rab6A to the Golgi apparatus in semi-intact HeLa cells: A role of BICD2 in stabilizing Rab6A on Golgi membranes and a concerted role of Rab6A/BICD2 interactions in Golgi-to-ER retrograde transport
Matsuto M, Kano F, *Murata M
Biochem. Biophys. Acta (Molecular Cell Research) 1853 , 2592–2609 (2015).
34.
Attolitre-sized lipid bilayer chamber array for rapid detection of single transporters
Soga N, *Watanabe R, *Noji H
Sci Rep 5 , 11025 (2015).
35.
Multitarget super-resolution microscopy with high-density labeling by exchangeable probes
*Kiuchi T, Higuchi M, Takamura A, Maruoka M, *Watanabe N
Nature Methods 12 , 743-746 (2015).
36.
Optically Detected Magnetic Resonance of Nanodiamonds In Vivo; Implementation of Selective Imaging and Fast Sampling
Yoshinari Y, Mori S, Igarashi R, Sugi T, Yokota H, Ikeda K, Sumiya H, Mori I, Tochio H, *Harada Y, *Shirakawa M
J Nanosci Nanotechnol 15 , 1014-1021(2015).
37.
Analysis of cell-surface receptor dynamics through covalent labeling by catalyst-tethered antibody
Hayashi T, Yasueda Y, Tamura T, Takaoka Y, *Hamachi I
J. Am. Chem. Soc. 137 , 5372–5380 (2015).
38.
Crystal Structures of SecYEG in Lipidic Cubic Phase Elucidate a Precise Resting and a Peptide-Bound State
Yoshiki Tanaka, Yasunori Sugano, Mizuki Takemoto, Takaharu Mori, Arata Furukawa, Tsukasa Kusakizako, Kaoru Kumazaki, Ayako Kashima, Ryuichiro Ishitani, Yuji Sugita, Osamu Nureki, *Tomoya Tsukazaki
Cell Rep 13 , 1561-1568 (2015).
39.
Sequential data assimilation for single-molecule FRET photon-counting data
Yasuhiro Matsunaga, Akinori Kidera, *Yuji Sugita
J. Chem. Phys. 142 , 214115 (2015).
40.
Domain motion enhanced (DoME) model for efficient conformational sampling of multidomain proteins
Chigusa Kobayashi, Yasuhiro Matsunaga, Ryotaro Koike, Motonori Ota, *Yuji Sugita
J. Phys. Chem. B 119 , 14584-14593 (2015).
41.
Hierarchical domain-motion analysis of conformational changes in sarcoplasmic reticulum Ca2+-ATPase
Chigusa Kobayashi, Ryotaro Koike, Motonori Ota, *Yuji Sugita
Proteins 83 , 746–756 (2015).
42.
GENESIS: A hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations
Jaewoon Jung, Takaharu Mori, Chigusa Kobayashi, Yasuhiro Matsunaga, Takao Yoda, Michael Feig, *Yuji Sugita
WIREs Comp. Mole. Sci. 5 , 310-323 (2015).
43.
Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory
Miki Nakano, Hisae Tateishi-Karimata, Shigenori Tanaka, Florence Tama, Osamu Miyashita, Shu-ichi Nakano, *Naoki Sugimoto.
Nucleic Acids. Res. 43 , 10114-10125 (2015).
44.
Crystal structures of SecYEG in lipidic cubic phase elucidate a precise resting and a peptide-bound states
Tanaka Y, Sugano Y, Takemoto M, Mori T, Furukawa A, Kusakizako T, Kumazaki K, Kashima A, Ishitani R, Sugita Y, *Nureki O, *Tsukazaki T
Cell Rep. 13 , 1561-1568 (2015).
45.
Hydrophilic microenvironment required for the channel-independent insertase function of YidC protein
Shimokawa N, Kumazaki K, Tsukazaki T, Nureki O, Ito K, *Chiba S
Proc. Natl. Acad. Sci. USA 112 , 5063-5068 (2015).
46.
Structural Analysis of Streptococcus pyogenes NADH Oxidase: Conformational Dynamics Involved in Formation of the C(4a)-Peroxyflavin Intermediate
Wallen JR, Mallett TC, Okuno T, Parsonage D, Sakai H, Tsukihara T, *Claiborne A
Biochemistry 54 , 6815-6829 (2015).
47.
Surface-enhanced IR absorption spectroscopy of the KcsA potassium channel upon application of an electric field
*Yamakata A., Shimizu H., *Oiki S
Phys. Chem. Chem. Phys. 17 , 21104-11(2015). 
48.
Specific interactions between alkali metal cations and the KcsA channel studied using ATR-FTIR spectroscopy
Furutani Y., Shimizu H., Asai Y., *Oiki S., *H. Kandori.
Biophys. Physicobiol. 12 , 37-45 (2015).
49.
pH-dependent promotion of phospholipid flip-flop by the KcsA potassium channel
Nakao H., Ikeda K., Iwamoto M, Shimizu H., Oiki S., Ishihama Y., *Nakano M
Biochim. Biophys. Acta-Biomembr. 1848 , 145-150 (2015).
50.
Weak interactions between Salmonella enterica FlhB and other flagellar export apparatus proteins govern type III secretion dynamics
*McMurry JL, Minamino T, Furukawa Y, Francis JW, Hill SA, Helms KA, Namba K
PLoS One 10 , e0134884 (2015).
51.
The bacterial flagellar motor and its structural diversity
*Minamino T, Imada K
Trends Microbiol. 23 , 267–274 (2015).
52.
Possible regulation of caveolar endocytosis and flattening by phosphorylation of F-BAR domain protein PACSIN2/Syndapin II
Senju Y, *Suetsugu S
Bioarchitecture. 5 , 70-77 (2015).
53.
Phosphorylation of PACSIN2 by protein kinase C triggers the removal of caveolae from the plasma membrane
Senju Y, Rosenbaum E, Shah C, Hamada-Nakahara S, Itoh Y, Yamamoto K, Hanawa-Suetsugu K, Daumke O, *Suetsugu S
J Cell Sci 128 , 2766-2780 (2015).
54.
Classification of projection images of proteins with structural polymorphism by manifold: A simulation study for X-ray fr, lectron laser diffraction imaging.
*Yoshidome T, Oroguchi T, Nakasako M, *Ikeguchi, M
Phys. Rev. E 92 , 032710 (13 pages) (2015).
55.
Structure of a thermophilic F1-ATPase inhibited by an γ–subunit: deeper insight into the γ–inhibition mechanism
*Shirakihara Y, Shiratori A, Tanikawa H, Nakasako M, Yoshida M, Suzuki T
FEBS Journal 282 , 2895-2913 (2015).
56.
Structure of the response regulator ChrA in the haem-sensing two-component system of Corynebacterium diphtheriae
Doi A, Nakamura H, Shiro Y, *Sugimoto H
Acta Crystallogr F Struct Biol Commun 71 , 966-971 (2015).



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